Genetic characterisation of a large antibiotic resistant environmental ST131 E. coli plasmid using a long read hybrid assembly approach

Escherichia coli Strain Type 131 are a globally disseminated environmental E. coli that has been linked to the capture and spread of plasmid mediated bla_CTX-M type extended spectrum beta-lactamase (ESBLs). Accurately identifying such resistance genes in their wider genetic context provides a greater understanding of the mechanisms of selection and persistence in the environment. In this study we use a novel DNA extraction and enrichment method in combination with a custom long-read scaffold hybrid-assembly and polishing pipe line to identify the genetic context of the plasmid borne bla_CTX-M gene previously identified in an ST131 environmental E. coli isolate.

This has allowed us to discern the complete structure of a ~100kb environmental plasmid and further resolve the bla_CTX-M variant to the group 9 bla_CTX-M-27 gene. The upstream IS26 insertion element associated with the global capture and dissemination of bla_CTX-M-15 was also identified in proximity to bla_CTX-M-27. Furthermore, the lack of conjugative machinery identified on this plasmid, in combination with a toxin-antitoxin and plasmid partitioning system, indicates a mechanism of vertical transmission to maintain persistence in a population.